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- PDB-2wl9: Crystal structure of catechol 2,3-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 2wl9
TitleCrystal structure of catechol 2,3-dioxygenase
ComponentsCATECHOL 2,3-DIOXYGENASE
KeywordsOXIDOREDUCTASE / AROMATIC HYDROCARBONS CATABOLISM / IRON
Function / homology
Function and homology information


dioxygenase activity / xenobiotic catabolic process / ferrous iron binding
Similarity search - Function
2,3-dihydroxybiphenyl 1,2-dioxygenase / Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. ...2,3-dihydroxybiphenyl 1,2-dioxygenase / Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / 3-METHYLCATECHOL / Catechol 2,3-dioxygenase
Similarity search - Component
Biological speciesRHODOCOCCUS SP. DK17 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCho, H.J. / Kim, K.J. / Kang, B.S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Substrate-Binding Mechanism of a Type I Extradiol Dioxygenase.
Authors: Cho, H.J. / Kim, K. / Sohn, S.Y. / Cho, H.Y. / Kim, K.J. / Kim, M.H. / Kim, D. / Kim, E. / Kang, B.S.
History
DepositionJun 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,04514
Polymers136,2734
Non-polymers77210
Water5,441302
1
C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules

C: CATECHOL 2,3-DIOXYGENASE
D: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,85724
Polymers272,5458
Non-polymers1,31216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area23010 Å2
ΔGint-204.3 kcal/mol
Surface area79680 Å2
MethodPISA
2
A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules

A: CATECHOL 2,3-DIOXYGENASE
B: CATECHOL 2,3-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,32332
Polymers272,5458
Non-polymers1,77724
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area24400 Å2
ΔGint-236.4 kcal/mol
Surface area78990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.562, 102.562, 142.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CATECHOL 2,3-DIOXYGENASE


Mass: 34068.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS SP. DK17 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6REQ5

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Non-polymers , 5 types, 312 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MBD / 3-METHYLCATECHOL / 3-METHYL-BENZENE-1,2-DIOL


Mass: 124.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 30% PEG 400. 0.1M HEPES PH7.5, 0.2M MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1
DetectorDate: Aug 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.508
11K, H, -L20.492
ReflectionResolution: 1.9→40 Å / Num. obs: 114402 / % possible obs: 99.2 % / Observed criterion σ(I): 1.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WL3

2wl3


Resolution: 1.9→142.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.922 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN B AND D RESIDUES 178-183 ARE DISORDERD
RfactorNum. reflection% reflectionSelection details
Rfree0.17602 5735 5 %RANDOM
Rwork0.15055 ---
obs0.15184 108666 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.827 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å20 Å2
2--4.3 Å20 Å2
3----8.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→142.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9348 0 41 302 9691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0219734
X-RAY DIFFRACTIONr_bond_other_d0.0070.0219734
X-RAY DIFFRACTIONr_angle_refined_deg1.071.94513241
X-RAY DIFFRACTIONr_angle_other_deg1.071.94513241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63551212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47323.738511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.419151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9691572
X-RAY DIFFRACTIONr_chiral_restr0.0710.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217754
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.55906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71729447
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07633828
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6634.53778
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 422 -
Rwork0.207 7821 -
obs--96.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37340.09540.01930.290.01760.50960.00890.0124-0.02670.00340.0153-0.04240.03490.0386-0.02410.0110.01050.00090.0158-0.01250.0334-29.498631.244233.5636
20.30340.0269-0.06470.48710.03290.41090.0105-0.0421-0.0250.03030.0091-0.06220.0210.0798-0.01960.01080.0024-0.01650.0551-0.00560.0271-21.72751.450272.0688
30.46710.0697-0.03170.1208-0.11520.3592-0.0096-0.01670.04320.01780.0222-0.024-0.0423-0.006-0.01260.0250.00480.00220.0155-0.02520.0462-4.909229.09090.5571
40.4458-0.0980.05650.40080.03120.57670.02480.02660.0575-0.02670.0126-0.0144-0.00820.0286-0.03740.026-0.00910.0170.01040.00210.028315.835524.9587-37.9407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 174
2X-RAY DIFFRACTION1A175 - 245
3X-RAY DIFFRACTION1A246 - 297
4X-RAY DIFFRACTION2B2 - 174
5X-RAY DIFFRACTION2B175 - 245
6X-RAY DIFFRACTION2B246 - 297
7X-RAY DIFFRACTION3C2 - 174
8X-RAY DIFFRACTION3C175 - 245
9X-RAY DIFFRACTION3C246 - 297
10X-RAY DIFFRACTION4D2 - 174
11X-RAY DIFFRACTION4D175 - 245
12X-RAY DIFFRACTION4D246 - 297

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